Category:Strain:BW25113: Difference between revisions

Latest revision as of 04:30, 13 August 2019

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Name	BW25113
Synonyms
Genotype	F^- DE(araD-araB)567 lacZ4787(del)::rrnB-3 LAM^- rph-1 DE(rhaD-rhaB)568 hsdR514
Phenotype
Plasmids
Phage
Sources	Coli Genetics Stock Center
Construction	see description below
References	PMID:10829079^[1] PMID:16738554^[2]
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Notes

BW25113 was used to make the Keio Collection of single-gene knockouts. ^[2] ^[1] BW25113 is available from the Coli Genetics Stock Center: CGSC#7636 The genotype for BW25113 in Datsenko et al. ^[1] said the strain is lacI^Q, but it was later shown to be lacI⁺ Baba et al. (Supplementary Table 1)^[2].

According to the CGSC, lacZ4787(del) has 4 tandem copies of the rrnB transcriptional terminator inserted by gene replacement into the region extending from near the SacII site near the N-terminus of lacZ through the promoter.

BW25113 is a derivative of E. coli K-12 strain BD792, which has the genotype F^- LAM^- rpoS396(Am) rph-1.

The steps in the construction of BW25113 are described below. This information is from Supplementary Table 1 of Baba et al.(^[2]). At several steps of the strain construction, mutant alleles were constructed in vitro and recombined into the genome using oriR_{R6K_gamma} plasmids, which cannot replicate in a strain that lacks the R6K pir gene (^[3]). In the absence of selection of the antibiotic resistance marker carried on the plasmid, homologous recombination can occur that will either restore the original genotype or result in allele replacement.

Step	Strain	Genotype	Construction	Reference
ii)	BW21597	F^- LAM^- rpoS396(Am) DEphoR574 rph-1	BD792 was made Tc^R with pAH14 then Tc^S Pho^- derivatives were isolated.^[4]	unpublished
iii)	BW21652	F^- LAM^- rpoS396(Am) DEphoR574 DE(creABCD)154 rph-1	BW21597 was made Tc^R with pSK26 and then Tc^S Cre^- derivatives were isolated. ^[3]	unpublished
iv)	BW23186	F^- LAM^- rpoS396(Am) DEphoR574 DE(creABCD)154 DE(araBAD)567 rph-1	BW21652 was made Tc^R with pAH54 and then Tc^S Ara^- derivatives were isolated. (^[5])	unpublished
v)	BW23599	F^- LAM^- rpoS396(Am) rrnB3 DElacZ4787 proC::Tn5-132 DE(creABCD)154 DE(araBAD)567 rph-1	BW23186 was transduced to Tc^R Pro^- Lac^- Pho⁺ with P1kc grown on BW22773^[5]	unpublished
vi)	BW23660	F^- LAM^- rpoS396(Am) rrnB3 DElacZ4787 DE(phoBR)580 DE(creABCD)154 DE(araBAD)567 rph-1	BW23599 was transduced to Pro⁺ Pho^- with P1kc grown on BW23316.	Haldimann et al. 1997^[4]
vii)	BW24200	F^- LAM^- rpoS396(Am) rrnB3 DElacZ4787 DE(phoBR)580 DE(creABCD)154 DE(araBAD)567 metF159(Am) zii-510::Tn10 rph-1	BW23660 was transduced to Tc^R Met^- with P1kc grown on JW383 (Haldimann et al., 1997)	unpublished
viii)	BW24201	F^- LAM^- rpoS396(Am) rrnB3 DElacZ4787 DE(phoBR)580 DE(creABCD)154 DE(araBAD)567 DE(rhaBAD)568 rph-1	BW24200 was transduced to Met⁺ Tc^S Rha^- with P1kc grown on BW22875^[5]	unpublished
ix)	BW24310	F^- LAM^- rrnB3 DElacZ4787 DE(phoBR)580 DE(creABCD)154 DE(araBAD)567 DE(rhaBAD)568 cysC95::Tn10 rpoS::kan rph-1	BW24201 was transduced to Tc^R Km^R with P1kc grown on ZK1001^[5]	Haldimann and Wanner, 2001^[6]
x)	BW24320^a	F^- LAM^- rrnB3 DElacZ4787 DE(phoBR)580 DE(creABCD)154 DE(araBAD)567 DE(rhaBAD)568 rph-1	BW24310 was transduced to Cys⁺ Km^S with P1kc grown on MG1655 (Wanner and Boline, 1990) ^aBW24320 and its descendants carry the same pseudorevertant rpoS(Q33) allele as MG1655 (Hayashi et al., 2005)	Haldimann and Wanner, 2001^[6]
xi)	BW24353	F^- LAM^- rrnB3 DElacZ4787 DE(phoBR)580 DE(zaa trpR creABCD arcA thr)104::Tn5-132 DE(araBAD)567 DE(rhaBAD)568 rph-1	BW24320 was transduced to Tc^R Thr^- with P1kc grown on BW12070 (Fisher et al., 1995)	unpublished
xii)	BW24476	F^- LAM^- rrnB3 DElacZ4787 DE(phoBR)580 hsdR514 DE(araBAD)567 DE(rhaBAD)568 rph-1	BW24353 was transduced to Thr⁺ HsdR^- with P1kc grown on BW24447^[7]	Stern et al., 1999^[7]
xiii)	BW25083	F^- LAM^- rrnB3 DElacZ4787 proC::Tn5-132 hsdR514 DE(araBAD)567 DE(rhaBAD)568 rph-1	BW24476 was transduced to Tc^R Pro^- Pho⁺ with P1kc grown on BW22773^[5]	Haldimann and Wanner, 2001^[6]
xiv)	BW25113	F^- LAM^- rrnB3 DElacZ4787 hsdR514 DE(araBAD)567 DE(rhaBAD)568 rph-1	BW25083 was transduced to Pro⁺ with P1kc grown on BW24321^[6]	Lessard et al., 1998^[8]; Datsenko and Wanner, 2000^[1]
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References

See Help:References for how to manage references in EcoliWiki.

↑ ^1.0 ^1.1 ^1.2 ^1.3 Datsenko, KA & Wanner, BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. U.S.A. 97 6640-5 PubMed
↑ ^2.0 ^2.1 ^2.2 ^2.3 Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
↑ ^3.0 ^3.1 Metcalf, WW et al. (1996) Conditionally replicative and conjugative plasmids carrying lacZ alpha for cloning, mutagenesis, and allele replacement in bacteria. Plasmid 35 1-13 PubMed
↑ ^4.0 ^4.1 Haldimann, A et al. (1997) Transcriptional regulation of the Enterococcus faecium BM4147 vancomycin resistance gene cluster by the VanS-VanR two-component regulatory system in Escherichia coli K-12. J. Bacteriol. 179 5903-13 PubMed
↑ ^5.0 ^5.1 ^5.2 ^5.3 ^5.4 Haldimann, A et al. (1998) Use of new methods for construction of tightly regulated arabinose and rhamnose promoter fusions in studies of the Escherichia coli phosphate regulon. J. Bacteriol. 180 1277-86 PubMed
↑ ^6.0 ^6.1 ^6.2 ^6.3 Haldimann, A & Wanner, BL (2001) Conditional-replication, integration, excision, and retrieval plasmid-host systems for gene structure-function studies of bacteria. J. Bacteriol. 183 6384-93 PubMed
↑ ^7.0 ^7.1 Stern, RJ et al. (1999) Conversion of dTDP-4-keto-6-deoxyglucose to free dTDP-4-keto-rhamnose by the rmIC gene products of Escherichia coli and Mycobacterium tuberculosis. Microbiology (Reading, Engl.) 145 ( Pt 3) 663-71 PubMed
↑ Lessard, IA et al. (1998) Homologs of the vancomycin resistance D-Ala-D-Ala dipeptidase VanX in Streptomyces toyocaensis, Escherichia coli and Synechocystis: attributes of catalytic efficiency, stereoselectivity and regulation with implications for function. Chem. Biol. 5 489-504 PubMed

Pages in category "Strain:BW25113"

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BW25113

[PMID:10829079-1] 1.0 ^1.1 ^1.2 ^1.3 Datsenko, KA & Wanner, BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. U.S.A. 97 6640-5 PubMed

[PMID:16738554-2] 2.0 ^2.1 ^2.2 ^2.3 Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed

[PMID:8693022-3] 3.0 ^3.1 Metcalf, WW et al. (1996) Conditionally replicative and conjugative plasmids carrying lacZ alpha for cloning, mutagenesis, and allele replacement in bacteria. Plasmid 35 1-13 PubMed

[PMID:9294451-4] 4.0 ^4.1 Haldimann, A et al. (1997) Transcriptional regulation of the Enterococcus faecium BM4147 vancomycin resistance gene cluster by the VanS-VanR two-component regulatory system in Escherichia coli K-12. J. Bacteriol. 179 5903-13 PubMed

[PMID:9495769-5] 5.0 ^5.1 ^5.2 ^5.3 ^5.4 Haldimann, A et al. (1998) Use of new methods for construction of tightly regulated arabinose and rhamnose promoter fusions in studies of the Escherichia coli phosphate regulon. J. Bacteriol. 180 1277-86 PubMed

[PMID:11591683-6] 6.0 ^6.1 ^6.2 ^6.3 Haldimann, A & Wanner, BL (2001) Conditional-replication, integration, excision, and retrieval plasmid-host systems for gene structure-function studies of bacteria. J. Bacteriol. 183 6384-93 PubMed

[PMID:10217500-7] 7.0 ^7.1 Stern, RJ et al. (1999) Conversion of dTDP-4-keto-6-deoxyglucose to free dTDP-4-keto-rhamnose by the rmIC gene products of Escherichia coli and Mycobacterium tuberculosis. Microbiology (Reading, Engl.) 145 ( Pt 3) 663-71 PubMed

[PMID:9751644-8] Lessard, IA et al. (1998) Homologs of the vancomycin resistance D-Ala-D-Ala dipeptidase VanX in Streptomyces toyocaensis, Escherichia coli and Synechocystis: attributes of catalytic efficiency, stereoselectivity and regulation with implications for function. Chem. Biol. 5 489-504 PubMed

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[2]

[3]

[4]

[5]

[6]

[7]

[8]

@@ Line 55: / Line 55: @@
 == Notes ==
-BW25113 is a derivative of the F<sup>-</sup>, λ<sup>-</sup>, ''E. coli'' K-12 strain [http://cgsc2.biology.yale.edu/Strain.php?ID=7024 BD792 (CGSC6159)]<ref name='PMID:10829079'/>, which is a derivative of ''E. coli'' K-12 W1485.  The steps in the construction of BW25113 are outlined below.
+BW25113 was used to make the Keio Collection of single-gene knockouts. <ref name=PMID:16738554/>
+<ref name=PMID:10829079/>  BW25113 is available from the Coli Genetics Stock Center: [http://cgsc2.biology.yale.edu/Strain.php?ID=64667 CGSC#7636]
+The genotype for BW25113 in Datsenko et al. <ref name=PMID:10829079/> said the strain is lacI<sup>Q</sup>, but it was later shown to be lacI<sup>+</sup> Baba et al. (Supplementary Table 1)<ref name=PMID:16738554/>.
-i) W1485 ([[http://cgsc2.biology.yale.edu/Strain.php?ID=5225 CGSC# 5024]]) genotype: F<sup>+</sup> LAM<sup>-</sup> rpoS396(Am) rph-1  -->
+According to the CGSC, ''lacZ4787(del)'' has 4 tandem copies of the rrnB transcriptional terminator inserted by gene replacement into the region extending from near the SacII site near the N-terminus of ''lacZ'' through the promoter.
-ii) BD792 ([[http://cgsc2.biology.yale.edu/Strain.php?ID=7024 CGSC# 6159]]) genotype: F<sup>-</sup> LAM<sup>-</sup> rpoS396(Am) rph-1. This is an F<sup>-</sup> derivative of W1485, cured with acridine orange. -->
-iii) An rpoS<sup>+</sup> derivative of BD792 was made in two steps. BD792 "was first made tetracycline resistant and kanamycin resistant by using P1kc grown on ZK1001 (cysC95::Tn10 rpoS::kan; from R. Kolter). A resultant Cys<sup>-</sup> transductant was then made cysteine independent and kanamycin sensitive by using P1kc grown on MG1655. E. coli K-12 strains BW25113, BW25141, BW25142, and BW25695 are descendants of BD792 derivatives that were made rpoS<sup>+</sup> (<ref name='PMID:11591683'/>)." -->
+BW25113 is a derivative of ''E. coli'' K-12 strain [http://cgsc2.biology.yale.edu/Strain.php?ID=7024 BD792], which has the genotype F<sup>-</sup> LAM<sup>-</sup> rpoS396(Am) rph-1.
-The remaining steps in the construction of BW25113 are described in Supplementary Table 1 of Baba et al. (<ref name='PMID:16738554'/>). At several steps, mutant alleles were constructed in vitro and recombined into the genome using oriR<sub>R6K<sub>gamma</sub></sub> plasmids, which cannot replicate in a strain that lacks the R6K ''pir'' gene (<ref name='PMID:8693022'/>). In the absence of selection of the antibiotic resistance marker carried on the plasmid, homologous recombination can occur that will either restore the original genotype or result in allele replacement.
+The steps in the construction of BW25113 are described below. This information is from Supplementary Table 1 of Baba et al.(<ref name='PMID:16738554'/>). At several steps of the strain construction, mutant alleles were constructed in vitro and recombined into the genome using oriR<sub>R6K<sub>gamma</sub></sub> plasmids, which cannot replicate in a strain that lacks the R6K ''pir'' gene (<ref name='PMID:8693022'/>). In the absence of selection of the antibiotic resistance marker carried on the plasmid, homologous recombination can occur that will either restore the original genotype or result in allele replacement.
 <!--box uid=b5af8a7dae3e04bf9589879451fcef19.182980.F5d50f998b2593-->
@@ Line 83: / Line 83: @@
 F<sup>-</sup> LAM<sup>-</sup> rpoS396(Am)  DEphoR574 rph-1
 |
-TcR with pAH14 then TcS and Pho- <ref name='PMID:9294451'/>
+BD792 was made Tc<sup>R</sup> with pAH14 then Tc<sup>S</sup> Pho<sup>-</sup> derivatives were isolated.<ref name='PMID:9294451'/>
 |
 unpublished
@@ Line 94: / Line 94: @@
 F<sup>-</sup> LAM<sup>-</sup> rpoS396(Am) DEphoR574 DE(creABCD)154 rph-1
 |
-TcR with pSK26 then TcS and Cre- <ref name='PMID:8693022'/>
+BW21597 was made Tc<sup>R</sup> with pSK26 and then Tc<sup>S</sup> Cre<sup>-</sup> derivatives were isolated. <ref name='PMID:8693022'/>
 |
 unpublished
@@ Line 105: / Line 105: @@
 F<sup>-</sup> LAM<sup>-</sup> rpoS396(Am) DEphoR574 DE(creABCD)154 DE(araBAD)567 rph-1
 |
-TcR with pAH54 the TcS and Ara- (<ref name='PMID:9495769'/>)
+BW21652 was made Tc<sup>R</sup> with pAH54 and then Tc<sup>S</sup> Ara<sup>-</sup> derivatives were isolated. (<ref name='PMID:9495769'/>)
 |
 unpublished
@@ Line 117: / Line 117: @@
 DE(araBAD)567 rph-1
 |
-transduced to TcR Pro- Lac- Pho+ with P1''kc'' grown on BW22773<ref name='PMID:9495769'/>
+BW23186 was transduced to Tc<sup>R</sup> Pro<sup>-</sup> Lac<sup>-</sup> Pho<sup>+</sup> with P1''kc'' grown on BW22773<ref name='PMID:9495769'/>
 |
 unpublished
@@ Line 128: / Line 128: @@
 F<sup>-</sup> LAM<sup>-</sup> rpoS396(Am) rrnB3 DElacZ4787 DE(phoBR)580 DE(creABCD)154 DE(araBAD)567 rph-1
 |
-Transduced to Pro+ Pho- with P1kc grown on BW23316
+BW23599 was transduced to Pro<sup>+</sup> Pho<sup>-</sup> with P1''kc'' grown on BW23316.
 |
 Haldimann et al. 1997<ref name='PMID:9294451'/>
@@ Line 140: / Line 140: @@
 DE(araBAD)567 metF159(Am) zii-510::Tn10 rph-1
 |
-transduced to TcR Met- with P1''kc'' grown on JW383 (Haldimann et al., 1997)
+BW23660 was transduced to Tc<sup>R</sup> Met<sup>-</sup> with P1''kc'' grown on JW383 (Haldimann et al., 1997)
 |
 unpublished
@@ Line 151: / Line 151: @@
 F<sup>-</sup> LAM<sup>-</sup> rpoS396(Am)  rrnB3 DElacZ4787 DE(phoBR)580 DE(creABCD)154 DE(araBAD)567 DE(rhaBAD)568 rph-1
 |
-transduced to Met+ TcS Rha- with P1''kc'' grown on BW22875<ref name='PMID:9495769'/>
+BW24200 was transduced to Met<sup>+</sup> Tc<sup>S</sup> Rha<sup>-</sup> with P1''kc'' grown on BW22875<ref name='PMID:9495769'/>
 |
 unpublished
@@ Line 162: / Line 162: @@
 F<sup>-</sup> LAM<sup>-</sup> rrnB3 DElacZ4787 DE(phoBR)580 DE(creABCD)154 DE(araBAD)567 DE(rhaBAD)568 cysC95::Tn10 rpoS::kan rph-1
 |
-transduced to TcR KmR with P1''kc'' grown on ZK1001<ref name='PMID:9495769'/>
+BW24201 was transduced to Tc<sup>R</sup> Km<sup>R</sup> with P1''kc'' grown on ZK1001<ref name='PMID:9495769'/>
 |
 Haldimann and Wanner, 2001<ref name='PMID:11591683'/>
@@ Line 173: / Line 173: @@
 F<sup>-</sup> LAM<sup>-</sup> rrnB3 DElacZ4787 DE(phoBR)580 DE(creABCD)154 DE(araBAD)567 DE(rhaBAD)568 rph-1
 |
-transduced to Cys+ KmS with P1''kc'' grown on MG1655 (Wanner and Boline, 1990)
+BW24310 was transduced to Cys<sup>+</sup> Km<sup>S</sup> with P1''kc'' grown on MG1655 (Wanner and Boline, 1990)
 <sup>a</sup>BW24320 and its descendants carry the same pseudorevertant rpoS(Q33) allele as MG1655 (Hayashi et al., 2005)
@@ Line 186: / Line 186: @@
 F<sup>-</sup> LAM<sup>-</sup> rrnB3 DElacZ4787 DE(phoBR)580 DE(zaa trpR creABCD arcA thr)104::Tn5-132 DE(araBAD)567 DE(rhaBAD)568 rph-1
 |
-Transduced to TcR Thr- with P1''kc'' grown on BW12070 (Fisher et al., 1995)
+BW24320 was transduced to Tc<sup>R</sup> Thr<sup>-</sup> with P1''kc'' grown on BW12070 (Fisher et al., 1995)
 |
 unpublished
@@ Line 197: / Line 197: @@
 F<sup>-</sup> LAM<sup>-</sup> rrnB3 DElacZ4787 DE(phoBR)580 hsdR514 DE(araBAD)567 DE(rhaBAD)568 rph-1
 |
-transduced to Thr+ HsdR- with P1''kc'' grown on BW24447<ref name='PMID:10217500'/>
+BW24353 was transduced to Thr<sup>+</sup> HsdR<sup>-</sup> with P1''kc'' grown on BW24447<ref name='PMID:10217500'/>
 |
 Stern et al., 1999<ref name='PMID:10217500'/>
@@ Line 208: / Line 208: @@
 F<sup>-</sup> LAM<sup>-</sup> rrnB3 DElacZ4787 proC::Tn5-132 hsdR514 DE(araBAD)567 DE(rhaBAD)568 rph-1
 |
-transduced to TcR Pro- Pho+ with P1''kc'' grown on BW22773<ref name='PMID:9495769'/>
+BW24476 was transduced to Tc<sup>R</sup> Pro<sup>-</sup> Pho<sup>+</sup> with P1''kc'' grown on BW22773<ref name='PMID:9495769'/>
 |
 Haldimann and Wanner, 2001<ref name='PMID:11591683'/>
@@ Line 219: / Line 219: @@
 F<sup>-</sup> LAM<sup>-</sup> rrnB3 DElacZ4787 hsdR514 DE(araBAD)567 DE(rhaBAD)568 rph-1
 |
-transduced to Pro+ with P1''kc'' grown on BW24321<ref name='PMID:11591683'/>
+BW25083 was transduced to Pro<sup>+</sup> with P1''kc'' grown on BW24321<ref name='PMID:11591683'/>
 |
 Lessard et al., 1998<ref name='PMID:9751644'/>; Datsenko and Wanner, 2000<ref name='PMID:10829079'/>
-|-
-|
-i)
-|
-BD792
-|
-F<sup>-</sup> LAM<sup>-</sup> rpoS396(Am) rph-1
-|
-An F- derivative of [http://cgsc2.biology.yale.edu/Strain.php?ID=5225 W1485] isolated after curing with acridine orange.
-|
-Wanner BL 1983<ref name='PMID:6304324'/>
 |- class="tableEdit_footer"
@@ Line 238: / Line 227: @@
 |}
 <!--box uid=b5af8a7dae3e04bf9589879451fcef19.182980.F5d50f998b2593-->
-BW25113 was used to make the Keio Collection of single-gene knockouts. <ref name=PMID:16738554/>
-<ref name=PMID:10829079/>  Available from the Coli Genetics Stock Center: [http://cgsc2.biology.yale.edu/Strain.php?ID=64667 CGSC#7636]
-The genotype for BW25113 in Datsenko et al. <ref name=PMID:10829079/> said the strain is lacI<sup>Q</sup>, but it was later shown to be lacI<sup>+</sup> Baba et al. (Supplementary Table 1)<ref name=PMID:16738554/>.
-According to the CGSC, ''lacZ4787(del)'' has 4 tandem copies of the rrnB transcriptional terminator inserted by gene replacement into the region extending from near the SacII site near the N-terminus of ''lacZ'' through the promoter.
 ==References==

Category:Strain:BW25113: Difference between revisions

Latest revision as of 04:30, 13 August 2019

Notes

References

Pages in category "Strain:BW25113"

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